Variant report
| Variant | rs4600612 |
|---|---|
| Chromosome Location | chr2:187990957-187990958 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | EP300 | chr2:187990853-187991826 | SK-N-SH | brain: | n/a | chr2:187991239-187991253 chr2:187991762-187991771 chr2:187990884-187990898 |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| RN7SKP42 | TF binding region |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs11890809 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs11891854 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs11894501 | 0.95[AFR][1000 genomes] |
| rs11896449 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs16828613 | 0.87[AFR][1000 genomes];0.87[AMR][1000 genomes] |
| rs16828645 | 0.89[YRI][hapmap] |
| rs4516390 | 0.89[YRI][hapmap] |
| rs55833494 | 0.95[AFR][1000 genomes] |
| rs6727719 | 1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs6756559 | 0.89[YRI][hapmap] |
| rs73979625 | 0.95[AFR][1000 genomes];0.87[AMR][1000 genomes] |
| rs73979631 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73979636 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73979642 | 0.92[AFR][1000 genomes];0.87[AMR][1000 genomes] |
| rs73979698 | 0.80[AFR][1000 genomes] |
| rs7602101 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv949700 | chr2:187713412-188361211 | Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv875553 | chr2:187856937-188067355 | Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv834486 | chr2:187876328-188032965 | Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS | TF binding regionChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 4 | nsv431857 | chr2:187930023-188098798 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 5 | nsv1003061 | chr2:187950057-188282330 | Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 6 | nsv1000617 | chr2:187950057-188290511 | Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:187990000-187991000 | Weak transcription | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
